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Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Authors: Rawlings ND, Barrett AJ, Bateman A Abstract MEROPS is a database of proteolytic enzymes as well as their inhibitors and substrates. Proteolytic enzymes and protein inhibitors are organized into protein domain families. In turn, families are organized into clans. Each peptidase, inhibitor, family, and clan has associated annotation, a multiple sequence alignment, a phylogenetic tree, literature references, and links to other databases. Interactions between proteolytic enzymes and inhibitors and between proteolytic enzymes and substrates are also presented. The entries in MEROPS are available via th...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using the structure-function linkage database to characterize functional domains in enzymes.
Authors: Brown S, Babbitt P Abstract The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. © 2014 by Jo...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Authors: Lopez R, Cowley A, Li W, McWilliam H Abstract The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of databases and analysis tools that are of key importance in bioinformatics. As well as providing Web interfaces to these resources, Web Services are available using SOAP and REST protocols that enable programmatic access to our resources and allow their integration into other applications and analytical workflows. This unit describes the various options available to a typical researcher or bioinformatician who wishes to use our resources via Web interface or programmatic...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Clustal omega.
Authors: Sievers F, Higgins DG Abstract Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment. © 2014 by John Wiley & Sons, Inc. ...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Genome Annotation and Curation Using MAKER and MAKER-P.
Authors: Campbell MS, Holt C, Moore B, Yandell M Abstract This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein-coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources. © 2014 by John Wiley & Sons, Inc. PMID: 25501943 [PubMed - in process] (Source: Current Proto...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents.
Authors: Petrotchenko EV, Makepeace KA, Borchers CH Abstract Cross-linking combined with mass spectrometry for the study of proteins and protein complexes is greatly facilitated by the use of isotopically coded cleavable cross-linking reagents. The isotopic coding of the cross-linker enables confident detection of the cross-link signals, while cleavage of the cross-linker provides masses of the individual peptides composing the cross-link and, therefore, facilitates unambiguous assignment of the cross-links. Here, we describe the DXMSMS Match program, designed for automatic analysis of LC-MS/MS mass spectr...
Source: Current Protocols in Bioinformatics - December 23, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

mtDNA Variation and Analysis Using MITOMAP and MITOMASTER.
Authors: Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC Abstract The MITOMAP database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The MITOMAP protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within MITOMAP is the powerful sequence analysis tool for hu...
Source: Current Protocols in Bioinformatics - December 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications.
Authors: Spencer JL, Bhatia VN, Whelan SA, Costello CE, McComb ME Abstract The identification of protein post-translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography-tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a program that was developed to facilitate the characterizatio...
Source: Current Protocols in Bioinformatics - November 30, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using VisANT to Analyze Networks.
Authors: Hu Z Abstract VisANT is a Web-based workbench for the integrative analysis of biological networks with unique features such as exploratory navigation of interaction network and multi-scale visualization and inference with integrated hierarchical knowledge. It provides functionalities for convenient construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation and drug target) relations from either the Predictome database or user-defined data ...
Source: Current Protocols in Bioinformatics - November 30, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.
Authors: Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA Abstract This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK....
Source: Current Protocols in Bioinformatics - November 30, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using SomaticSniper to Detect Somatic Single Nucleotide Variants.
Authors: Larson DE, Abbott TE, Wilson RK Abstract Detecting somatic single nucleotide variants (SNVs) is an essential component of cancer research with next generation sequencing data. This protocol describes how to run the SomaticSniper somatic SNV detector and then filter the output to eliminate most false positives. It also includes support protocols detailing the compilation of the software. PMID: 25431635 [PubMed - as supplied by publisher] (Source: Current Protocols in Bioinformatics)
Source: Current Protocols in Bioinformatics - November 30, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Searching NCBI databases using Entrez.
Authors: Baxevanis AD Abstract One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text-b...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using VMD: an introductory tutorial.
Authors: Hsin J, Arkhipov A, Yin Y, Stone JE, Schulten K Abstract VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the t...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Using AutoDock for ligand-receptor docking.
Authors: Morris GM, Huey R, Olson AJ Abstract This unit describes how to set up and analyze ligand-protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X-ray crystal structure of Indinavir bound to HIV-1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research

Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype.
Authors: Shaw DR Abstract The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, mammalian orthologies, SNPs and PCR polymorphisms, mapping data, and links to other bioinformatics databases. Data integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Di...
Source: Current Protocols in Bioinformatics - November 12, 2014 Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research